Cancer is the second leading cause of death in industrial countries. More than 70% of all cancer deaths are due to carcinomas, i.e., cancers of epithelial organs. Most carcinoma tumors show initial or compulsory chemoresistance. This property makes it very difficult to cure these tumors when they are detected in progressed stages. Primary forms of liver cancers include hepatocellular carcinoma, biliary tract cancer and hepatoblastoma. Hepatocellular carcinoma is the fifth most common cancer worldwide but, owing to the lack of effective treatment options, constitutes the leading cause of cancer deaths in Asia and Africa and the third leading cause of cancer death worldwide. Parkin et al. “Estimating the world cancer burden: Globocan 2000.” Int. J. Cancer 94, 153-156 (2001).
The risk factors for liver cancer include excessive alcohol intake or other toxins, such as iron, aflatoxin B1 and also the presence of other infections such as hepatitis B and C. Alison & Lovell. “Liver cancer: the role of stem cells.” Cell Prolif. 38, 407-421 (2005). The only curative treatments for hepatocellular carcinoma are surgical resection or liver transplantation, but most patients present with advanced disease and are not candidates for surgery. To date, systemic chemotherapeutic treatment is ineffective against hepatocellular carcinoma, and no single drug or drug combination prolongs survival. Llovet. et al. “Hepatocellular carcinoma.” Lancet 362, 1907-1917. (2003). However, despite its clinical significance, liver cancer is understudied relative to other major cancers.
One of the difficulties in identifying appropriate therapeutics for tumor cells in vivo is the limited availability of appropriate test material. Human tumor lines grown as xenographs are unphysiological, and the wide variation between human individuals, not to mention treatment protocols, makes clinical studies difficult. Consequently, oncologists are often forced to perform correlative studies with a limited number of highly dissimilar samples, which can lead to confusing and unhelpful results.
Non-human animal models provide a useful alternative to studies in humans and to human tumor cell lines grown as xenographs, as large numbers of genetically-identical individuals can be treated with identical regimens. Moreover, the ability to introduce germline mutations that affect oncogenesis into these animals increases the power of the models.
To investigate the basic mechanisms of carcinogenesis and to test new potential cancer agents and therapies, however, realistic carcinoma-non-human animal models are urgently needed. So far there have been two major ways to create carcinoma non-human animal models: (i) the generation of transgenic or chimeric non-human animals that express oncogenes under the control of a tissue specific promoter and (ii) carcinomas that were induced by chemical carcinogens. Both approaches have several disadvantages.
Current animal models for cancer are based largely on classical transgenic approaches that direct expression of a particular oncogene to an organ of choice using a tissue specific promoter. See, e.g., Wang et al. “Activation of the Met receptor by cell attachment induces and sustains hepatocellular carcinomas in transgenic mice.” J. Cell Biol. 153, 1023-1034 (2001). Although such models have provided important insights into the pathogenesis of cancer, they express the active oncogene throughout the entire organ, a situation that does not mimic spontaneous tumorigenesis. Moreover, incorporation of additional lesions, such as a second oncogene or loss of a tumor suppressor, requires genetic crosses that are time consuming and expensive, and again produce whole tissues that are genetically altered. Finally, traditional transgenic and knockout strategies do not specifically target liver progenitor cells, which may be the relevant initiators of the disease.
Cancer therapies that directly target oncogenes are based on the premise that cancer cells require continuous oncogenic signaling for survival and proliferation. Non-human animal models expressing oncogenes in genetic backgrounds that lack, or have down-regulated, tumor suppressor genes can thus serve as valuable tools to study tumor initiation, maintenance, progression, treatment and regression. However, responses to the targeting drugs are often heterogeneous, and chemoresistance and other resistance is a problem. Because most anticancer agents were discovered through empirical screens, efforts to overcome resistance are hindered by a limited understanding of why these agents are effective and when and how they become less or non-effective.
Furthermore, although cancer usually arises from a combination of mutations in oncogenes and tumor suppressor genes, the extent to which tumor suppressor gene loss is required for the maintenance of established tumors is poorly understood.
Variations in both non-human animal strains and promoters used to drive expression of oncogenes complicate the interpretation of cancer mechanistics and treatment analyses. Firstly, intercrossing strategies to obtain non-human animals of the desired genetic constellation are extremely time consuming and costly. Secondly, the use of certain cell-selective promoters can result in a cell-bias for tumor initiation. For example, the mouse mammary tumor virus (MMTV) promoter and the Whey Acidic Protein (WAP) promoter are commonly used to model breast cancer development in mice, and yet may not target all subtypes of mammary epithelia, i.e., stem cell and non-stem cells. Finally, a homogenous expression of the respective oncogene in all epithelial cells of an organ creates an unphysiological condition, as tumors are known to originate within genetic-mosaics.
An additional difficulty in identifying and evaluating the efficacy of cancer agents on tumor cells and understanding the molecular mechanisms of the cancers and their treatment in the current non-human animal models in vivo is the limited availability of appropriate material.
It is therefore important to use a valid model to identify new therapeutics for the treatment of liver cancer.
Investigation of the role of oncogenes or tumor suppressor genes in tumorigenesis can be facilitated by specifically silencing, or preventing from exerting its presence, the particular gene of interest. One such silencing means is through “RNA interference” or “RNAi.” RNAi stems from a phenomenon observed in plants and worms whereby double-stranded RNA (dsRNA) blocks gene expression in a specific and post-transcriptional manner. The dsRNA is cleaved by an RNAse III enzyme “DICER” into a 21-23 nucleotide small interfering RNA (siRNA). These siRNAs are incorporated into a RNA-induced silencing complex (RISC) that identifies and silences RNA complimentary to the siRNA. Without being bound by theory, RNAi appears to involve silencing of cytoplasmic mRNA by triggering an endonuclease cleavage, promoting translation repression, or possibly accelerating mRNA decapping (Valencia-Sanchez et al., 2006, Genes & Development 20: 515-524). Biochemical mechanisms of RNAi are currently an active area of research.
Three mechanisms of utilizing RNAi in mammalian cells have been described. The first is cytoplasmic delivery of siRNA molecules, which are either chemically synthesized or generated by DICER-digestion of dsRNA. These siRNAs are introduced into cells using standard transfection methods. The siRNAs enter the RISC complex to silence target mRNA expression.
The second mechanism is nuclear delivery, via viral vectors, of gene expression cassettes expressing a short hairpin RNA (shRNA). The shRNA is modeled on micro interfering RNA (miRNA), an endogenous trigger of the RNAi pathway (Lu et al., 2005, Advances in Genetics 54: 117-142, Fewell et al., 2006, Drug Discovery Today 11: 975-982). The endogenous RNAi pathway is comprised of three RNA intermediates: a long, largely single-stranded primary miRNA transcript (pri-mRNA), a precursor miRNA transcript having a stem-and-loop structure and derived from the pri-mRNA (pre-miRNA), and a mature miRNA. The miRNA gene is transcribed by an RNA polymerase II promoter into the pri-mRNA transcript, which is then cleaved to form the pre-miRNA transcript (Fewell et al., supra). The pre-miRNA is transported to the cytoplasm and is cleaved by DICER to form mature miRNA. miRNA then interacts with the RISC in the same manner as siRNA. shRNAs, which mimic pre-miRNA, are transcribed by RNA Polymerase II or III as single-stranded molecules that form stem-loop structures. Once produced, they exit the nucleus, are cleaved by DICER, and enter the RISC complex as siRNAs.
The third mechanism is identical to the second mechanism, except that the shRNA is modeled on pri-miRNA (shRNAmir), rather than pre-miRNA transcripts (Fewell et al., supra). An example is the miR-30 miRNA construct. The use of this transcript produces a more “physiological” shRNA that reduces toxic effects. The shRNAmir is first cleaved to produce shRNA, and then cleaved again by DICER to produce siRNA. The siRNA is then incorporated into the RISC for target mRNA degradation.
RNAi has been used to successfully identify and suppress target genes associated with tumorigenesis. For example, expression of microRNA-based shRNA specific to Trp53 produces “potent, stable, and regulatable gene knock-down in cultured cells . . . even when present at a single copy in the genome” (Dickins et al., 2005, Nature Genetics 37: 1289-1295). The tumors induced by the p53 knockdown regress upon re-expression of Trp53. Id. The suppression of the Trp53 gene expression by shRNA is also possible in stem cells and reconstituted organs derived from those cells (Hemann et al., 2003, Nature Genetics 33: 396-400). Moreover, the extent of inhibition of p53 function by the shRNA correlates with the type and severity of subsequent lymphomagenesis. Id.
However, there are conflicting views on which method of introducing and using RNAi mechanism is most effective. Some studies emphasize siRNA's several drawbacks, including transient effects, difficulty in delivery to nondividing primary cells, and concentration-dependent off-target effects. shRNAs expressed from viral vectors “are more versatile, allowing . . . stable integration, germline transmission, and the creation of in vivo animal models (Fewell et al., supra). shRNA is also more suitable for hard-to-transfect cells, due to its infection-based delivery, and has decreased concentration-dependent off-target effects. Id. In comparison with shRNA, shRNAmir is more efficiently processed into siRNA and produces a more consistent silencing of mRNA than shRNA. Id.
Despite the advantages of shRNA, other studies maintain that use of siRNA for RNAi purposes is emerging more rapidly than the use of shRNA (Lu et al., supra), partly because of the “increased effort required to construct shRNA expression systems before selection of active sequences and verification of biological activity are obtained.” Id. It is often time consuming and expensive to both construct shRNA expression cassettes and incorporate them into viral delivery systems. Id. On the contrary, use of synthetic oligonucleotides allows for rapid screening and studying of siRNA sequences and matching genes. Id. Moreover, recent studies investigating in vivo applications of RNAi focus on non-viral delivery of siRNA constructs as opposed to viral delivery of shRNA constructs, as viral vectors often raise concerns about safety and immunogenecity (Lu et al., supra; Vohies et al., 2007, Expert Rev. Anticancer Ther. 7: 373-382). In sum, there is no established method of RNAi that consistently produces the most effective RNA silencing.
Studies also vary in their use of genome-wide collections of pooled shRNA vectors versus small sets of shRNA vectors that target a specific gene family. The use of large shRNA libraries may lead to difficulties in measuring the relative abundance of each individual shRNA vector in a complex population of cells infected with thousands of vectors. In addition, the smaller scaled experiments allow “screening for relatively labor-intensive phenotypes.” Id. Pooled screens also pose several technological hurdles, such as obtaining uniform pools of viruses, creating robust design algorithms that enable gene knockdown at a single-copy level, and preventing large numbers of false positives (Fewell et al., supra). On the other hand, the use of barcodes, or unique sequence of nucleotides incorporated into each shRNA vector, allows for more accurate quantification of specific shRNAs in pooled analyses (Bernards et al., 2006, Nature Methods 3: 701-706). Moreover, larger shRNA library screens can be used to select for long-term phenotypes while smaller shRNA screens are mainly limited to “short-term” readouts. Id. Given the various benefits and drawbacks of both large and small scale screens, there is no suggestion that use of one method or the other is the most effective strategy for successful RNAi.
Finally, although certain tumor suppressors such as p53 are well-studied, the importance of other individual tumor suppressors is still unknown. As such, the extent of overall tumor suppressor gene loss required for maintaining tumors is poorly understood. Moreover, although there is potential to utilize Myc overexpression to investigate novel tumor suppressor genes, few scientists have so far been able to do so.
Established approaches for the investigation of novel oncogenes and tumor suppressor genes using RNAi are thus unavailable. As such, the invention described herein will further elucidate the mechanism of tumorigenesis and promote the development of treatment methods based on such understanding.